Francisco, This isn't really a job that Artemis was designed for. That is, you do not want to do a path-by-path analysis. I think what you want is to write a script that runs Feff on your several hundreds of configuration, and then extract and sum the chi.dat files from each of the runs. Feff itself is rather clumsy for this purpose, as it uses files with fixed names ("feff.inp", "chi.dat"), and so each run needs to be done in a separate directory. As you say, it's mostly a book-keeping problem. For EXAFS and in these days of multi-core machines, I would not worry too much about doing a "full feff calculation". That is, it might be possible to save some time by not recalculating Feff potentials for each run, but this may not be a huge overhead. You probably want to run with "configurational averaging" (that is, using all Zn atoms in a cluster as the absorber). I would recommend carefully testing this -- I believe that several versions of Feff have claimed to do such configurational averages and have not done this correctly. For your case, if you get a Zn-O coordination of 6.00 for every configuration, you'll know ithe averaging is wrong ;). In that case, you may need to run Feff separately for each Zn central atom for each of your snapshots / clusters. Perhaps the RMCProfile code can take care of all of this. Sadly, although this code was written for the US Government and so is required to be placed in the Public Domain, and although this code apparently makes use of the Open Source code of Ifeffit and Artemis, I could not download the code, as following all links leads to asking for a password to get the software. Hope that helps, --Matt On Tue, Apr 12, 2011 at 1:51 PM, Francisco Garcia wrote:

Dear Anatoly,

Thank you very much for your reply. Unfortunately, your PRB references did not solve my problems. I am trying to reproduce the results of Cauet et al [J. Chem. Phys. 132, 194502 (2010)]. I basically have over 500 snapshots of a single Zn2+ ion (absorbing atom) in water (O atoms are the scattering atoms). I have the feff.inp file for each snapshot ready for Artemis. I basically want an efficient way to obtain the chi(k) of data for each snapshot and average the chi(k) as opposed to loading the feff.inp files one by one. Specifically a sample script/example will be of imense help. I could not find much information in the Artemis user manual. I must also state that I am an EXAFS novice so a step by step explanation will help me a lot.

Thank you very much. _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

If you use Matlab and have feff*.exe, I have a script that does feff calculation for each snapshot and move all files to designated directories. It takes about an hour to do 100 snapshots in my PC. So you need to run it for a while. Yuan On 4/12/11 11:51 AM, "Francisco Garcia" wrote:

Dear Anatoly,

Thank you very much for your reply. Unfortunately, your PRB references did not solve my problems. I am trying to reproduce the results of Cauet et al [J. Chem. Phys. 132, 194502 (2010)]. I basically have over 500 snapshots of a single Zn2+ ion (absorbing atom) in water (O atoms are the scattering atoms). I have the feff.inp file for each snapshot ready for Artemis. I basically want an efficient way to obtain the chi(k) of data for each snapshot and average the chi(k) as opposed to loading the feff.inp files one by one. Specifically a sample script/example will be of imense help. I could not find much information in the Artemis user manual. I must also state that I am an EXAFS novice so a step by step explanation will help me a lot.

Thank you very much. _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit